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Auxiliary R scripts of the IntaRNA package

IntaRNA_CSV_p-value.R

p-value estimates of IntaRNA energies from present energy distribution

For genome-wide target sRNA predictions, we assume the set of energy values predicted for all target sufficiently diverse to be used as a background energy model for minimum energies of putative target sequences. Thus, we can fit a generalized extreme value (GEV) distribution to the data that is subsequently used to estimate p-values for each energy.

The IntaRNA_CSV_p-value.R script takes an IntaRNA CSV output file (assumed to be sufficiently large and sane enough for GEV fitting) to compute respective p-value estimates. The output consists of the input table extended with a p-value column. If no output file is given or in- and output file names are equal, the input file is overwritten! You can (optionally) specify the column name for which p-values are to be estimated. Example calls are given below.

# overwriting the input file with p-value-extended table
Rscript --vanilla IntaRNA_CSV_p-value.R IntaRNA-output.csv
# creating a new output file for p-value extension
Rscript --vanilla IntaRNA_CSV_p-value.R IntaRNA-output.csv IntaRNA-output-with-pValue.csv
# computing p-values for normalized energies (has to be present in file IN.csv)
Rscript --vanilla IntaRNA_CSV_p-value.R IN.csv IN-pValue.csv E_norm

IntaRNA_plotRegions.R

Visualization of RRI-covered regions

To visualize sequences' regions covered by RNA-RNA interactions predicted by IntaRNA, you can use IntaRNA_plotRegions.R by providing the following arguments (in the given order)

  1. CSV-IntaRNA output file (semicolon separated) covering the columns start,end,id with suffix 1 or 2 to plot target or query regions, respectively
  2. 1 or 2 to select whether to plot target or query regions
  3. output file name with a file-format-specific suffix from .pdf, .png, .svg, .eps, .ps, .jpeg, .tiff

An example is given below, when calling

Rscript --vanilla IntaRNA_plotRegions.R pred.csv 1 plotRegions.example.png

with pred.csv containing

id1;start1;end1;id2;start2;end2
b0001;266;273;query;116;123
b0002;204;231;query;85;111
b0003;229;262;query;96;125
b0004;265;300;query;10;38
b0005;281;295;query;5;22

will produce the output IntaRNA_plotRegions.R example